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- PDB-4udd: GR in complex with desisobutyrylciclesonide -

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Basic information

Entry
Database: PDB / ID: 4udd
TitleGR in complex with desisobutyrylciclesonide
Components
  • GLUCOCORTICOID RECEPTOR
  • NUCLEAR RECEPTOR COACTIVATOR 2
KeywordsSIGNALING PROTEIN / NUCLEAR HORMONE RECEPTOR / LIGAND COMPLEX / PEPTIDE COMPLEX
Function / homology
Function and homology information


Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / glucocorticoid metabolic process / response to cortisol / PTK6 Expression / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / glucocorticoid metabolic process / response to cortisol / PTK6 Expression / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation / maternal behavior / astrocyte differentiation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / adrenal gland development / regulation of gluconeogenesis / cellular response to glucocorticoid stimulus / cellular response to steroid hormone stimulus / locomotor rhythm / motor behavior / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cellular response to transforming growth factor beta stimulus / core promoter sequence-specific DNA binding / cellular response to hormone stimulus / transcription regulator inhibitor activity / Recycling of bile acids and salts / positive regulation of adipose tissue development / steroid binding / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / cellular response to dexamethasone stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / response to progesterone / TBP-class protein binding / Activation of gene expression by SREBF (SREBP) / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / nuclear receptor binding / negative regulation of smoothened signaling pathway / synaptic transmission, glutamatergic / chromosome segregation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Hsp90 protein binding / mRNA transcription by RNA polymerase II / circadian regulation of gene expression / promoter-specific chromatin binding / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / response to wounding / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle / RNA polymerase II transcription regulator complex / nuclear receptor activity / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / : / HATs acetylate histones / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / Estrogen-dependent gene expression / Potential therapeutics for SARS / gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / protein dimerization activity / nuclear speck / nuclear body / mitochondrial matrix / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / cell division / negative regulation of DNA-templated transcription / apoptotic process / synapse / centrosome / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator ...Glucocorticoid receptor / Glucocorticoid receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / : / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DESISOBUYTYRYL CICLESONIDE / Glucocorticoid receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEdman, K. / Hogner, A. / Hussein, A. / Bjursell, M. / Aagaard, A. / Backstrom, S. / Bodin, C. / Wissler, L. / Jellesmark-Jensen, T. / Cavallin, A. ...Edman, K. / Hogner, A. / Hussein, A. / Bjursell, M. / Aagaard, A. / Backstrom, S. / Bodin, C. / Wissler, L. / Jellesmark-Jensen, T. / Cavallin, A. / Karlsson, U. / Nilsson, E. / Lecina, D. / Takahashi, R. / Grebner, C. / Lepisto, M. / Guallar, V.
CitationJournal: Structure / Year: 2015
Title: Ligand Binding Mechanism in Steroid Receptors: From Conserved Plasticity to Differential Evolutionary Constraints.
Authors: Edman, K. / Hosseini, A. / Bjursell, M.K. / Aagaard, A. / Wissler, L. / Gunnarsson, A. / Kaminski, T. / Kohler, C. / Backstrom, S. / Jensen, T.J. / Cavallin, A. / Karlsson, U. / Nilsson, E. ...Authors: Edman, K. / Hosseini, A. / Bjursell, M.K. / Aagaard, A. / Wissler, L. / Gunnarsson, A. / Kaminski, T. / Kohler, C. / Backstrom, S. / Jensen, T.J. / Cavallin, A. / Karlsson, U. / Nilsson, E. / Lecina, D. / Takahashi, R. / Grebner, C. / Geschwindner, S. / Lepisto, M. / Hogner, A.C. / Guallar, V.
History
DepositionDec 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOCORTICOID RECEPTOR
B: NUCLEAR RECEPTOR COACTIVATOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2737
Polymers33,8962
Non-polymers2,3775
Water4,504250
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-10.5 kcal/mol
Surface area13530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.200, 87.200, 102.887
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein GLUCOCORTICOID RECEPTOR / GR / NUCLEAR RECEPTOR SUBFAMILY 3 GROUP C MEMBER 1


Mass: 32187.139 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 500-777 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC1 / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P04150
#2: Protein/peptide NUCLEAR RECEPTOR COACTIVATOR 2 / NCOA-2 / CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 75 / BHLHE75 / TRANSCRIPTIONAL INTERMEDIARY FACTOR ...NCOA-2 / CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 75 / BHLHE75 / TRANSCRIPTIONAL INTERMEDIARY FACTOR 2 / HTIF2 / NCOA2


Mass: 1708.931 Da / Num. of mol.: 1 / Fragment: RESIDUES 740-753 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q15596

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Non-polymers , 4 types, 255 molecules

#3: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CV7 / DESISOBUYTYRYL CICLESONIDE


Mass: 470.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H38O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.79 % / Description: NONE
Crystal growpH: 7.5
Details: 10% PEG8000, 20% ETHYLENE GLYCOL, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→40.1 Å / Num. obs: 42444 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 30.14 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.4
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 0.7 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M2Z

1m2z


Resolution: 1.8→40.14 Å / Cor.coef. Fo:Fc: 0.9493 / Cor.coef. Fo:Fc free: 0.9409 / SU R Cruickshank DPI: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.113 / SU Rfree Blow DPI: 0.102 / SU Rfree Cruickshank DPI: 0.099
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 2138 5.05 %RANDOM
Rwork0.2126 ---
obs0.2132 42339 99.84 %-
Displacement parametersBiso mean: 36.19 Å2
Baniso -1Baniso -2Baniso -3
1--3.9039 Å20 Å20 Å2
2---3.9039 Å20 Å2
3---7.8078 Å2
Refine analyzeLuzzati coordinate error obs: 0.302 Å
Refinement stepCycle: LAST / Resolution: 1.8→40.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 146 250 2540
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012392HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.063272HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d894SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes322HARMONIC5
X-RAY DIFFRACTIONt_it2392HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion14.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion327SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3162SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5317 144 4.66 %
Rwork0.516 2943 -
all0.5168 3087 -
obs--99.84 %

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